# Package picard.illumina.parser.readers

package picard.illumina.parser.readers

Related Packages
Package
Description
picard.illumina.parser
picard.illumina.parser.fakers
Class
Description
AbstractIlluminaPositionFileReader
The position files of Illumina are nearly the same form: Pos files consist of text based tabbed x-y coordinate float pairs, locs files are binary x-y float pairs, clocs are compressed binary x-y float pairs.
BarcodeFileReader
Reads a single barcode file line by line and returns the barcode if there was a match or NULL otherwise.
BaseBclReader
BclIndexReader
Annoyingly, there are two different files with extension .bci in NextSeq output.
BclQualityEvaluationStrategy
Describes a mechanism for revising and evaluating qualities read from a BCL file.
BclReader
BCL Files are base call and quality score binary files containing a (base,quality) pair for successive clusters.
CbclReader
------------------------------------- CBCL Header ----------------------------------- Bytes 0 - 1 Version number, current version is 1 unsigned 16 bits little endian integer Bytes 2 - 5 Header size unsigned 32 bits little endian integer Byte 6 Number of bits per basecall unsigned Byte 7 Number of bits per q-score unsigned
ClocsFileReader
The clocs file format is one of 3 Illumina formats(pos, locs, and clocs) that stores position data exclusively.
EmpiricalPhasingMetricsOutReader
EmpiricalPhasingMetricsOutReader.IlluminaPhasingMetrics
FilterFileReader
Illumina uses an algorithm described in "Theory of RTA" that determines whether or not a cluster passes filter("PF") or not.
LocsFileReader
The locs file format is one 3 Illumina formats(pos, locs, and clocs) that stores position data exclusively.
MMapBackedIteratorFactory
MMapBackedIteratorFactory a file reader that takes a header size and a binary file, maps the file to a read-only byte buffer and provides methods to retrieve the header as it's own bytebuffer and create iterators of different data types over the values of file (starting after the end of the header).
PosFileReader
The pos file format is one 3 Illumina formats(pos, locs, and clocs) that stores position data exclusively.
TileMetricsOutReader
Reads a TileMetricsOut file commonly found in the InterOp directory of an Illumina Run Folder.
TileMetricsOutReader.IlluminaLaneTileCode
Helper class which captures the combination of a lane, tile & metric code
TileMetricsOutReader.IlluminaTileMetrics
IlluminaPhasingMetrics corresponds to a single record in a TileMetricsOut file
TileMetricsOutReader.TileMetricsVersion